Chemical Components in the PDB

pdbe.org/chem
spacer

1F5 : Summary

Code

1F5

One-letter code

X

Molecule name

(1R,3aS,4R,5R,6R,9aR,10E)-6-({(1S,2R,4S,5R,6R,8S,9S)-5-hydroxy-2-(methoxymethyl)-9-methyl-9-[(2S)-oxiran-2-yl]-3,7,10,11-tetraoxatricyclo[6.2.1.0~1,6~]undec-4-yl}oxy)-1-(methoxymethyl)-4,9a-dimethyl-7-(propan-2-yl)-1,2,3,3a,4,5,6,8,9,9a-decahydrodicyclopenta[a,d][8]annulene-1,5-diol

Synonyms

Cotylenin A

Systematic names

ProgramVersionName
ACDLabs 12.01 (1R,3aS,4R,5R,6R,9aR,10E)-6-({(1S,2R,4S,5R,6R,8S,9S)-5-hydroxy-2-(methoxymethyl)-9-methyl-9-[(2S)-oxiran-2-yl]-3,7,10,11-tetraoxatricyclo[6.2.1.0~1,6~]undec-4-yl}oxy)-1-(methoxymethyl)-4,9a-dimethyl-7-(propan-2-yl)-1,2,3,3a,4,5,6,8,9,9a-decahydrodicyclopenta[a,d][8]annulene-1,5-diol (non-preferred name)

Formula

C33 H50 O11

Formal charge

0

Molecular weight

622.743 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 O4C(C5OC6C(O)C(OC3C1=C(C(C)C)CCC1(C=C2C(O)(COC)CCC2C(C)C3O)C)OC(C46O5)COC)(C7OC7)C
SMILES CACTVS 3.370 COC[CH]1O[CH](O[CH]2[CH](O)[CH](C)[CH]3CC[C](O)(COC)C3=C[C]4(C)CCC(=C24)C(C)C)[CH](O)[CH]5O[CH]6O[C]15O[C]6(C)[CH]7CO7
SMILES OpenEye OEToolkits 1.7.6 CC1C2CCC(C2=CC3(CCC(=C3C(C1O)OC4C(C5C6(C(O4)COC)OC(O5)C(O6)(C)C7CO7)O)C(C)C)C)(COC)O
Canonical SMILES CACTVS 3.370 COC[C@H]1O[C@H](O[C@H]2[C@H](O)[C@H](C)[C@@H]\3CC[C@](O)(COC)C\3=C/[C@@]4(C)CCC(=C24)C(C)C)[C@H](O)[C@H]5O[C@H]6O[C@@]15O[C@@]6(C)[C@@H]7CO7
Canonical SMILES OpenEye OEToolkits 1.7.6 C[C@@H]1[C@@H]\2CC[C@@](/C2=C/[C@]3(CCC(=C3[C@H]([C@@H]1O)O[C@@H]4[C@@H]([C@@H]5[C@]6([C@H](O4)COC)O[C@H](O5)[C@](O6)(C)[C@@H]7CO7)O)C(C)C)C)(COC)O

IUPAC InChI

InChI=1S/C33H50O11/c1-16(2)18-8-10-30(4)12-20-19(9-11-32(20,36)15-38-7)17(3)24(34)26(23(18)30)41-28-25(35)27-33(22(40-28)13-37-6)43-29(42-27)31(5,44-33)21-14-39-21/h12,16-17,19,21-22,24-29,34-36H,8-11,13-15H2,1-7H3/b20-12+/t17-,19+,21+,22-,24-,25-,26-,27-,28-,29+,30-,31+,32+,33-/m1/s1

IUPAC InChI key

SMQRKTIIIYTOTN-XWJJHAMOSA-N
1F5

wwPDB Information

Atom count

94 (44 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2013-01-11

Last modified at

2013-09-20

Status

Released

Obsoleted

Not Assigned



1F5 : Atoms of Molecule

Total Number of Atoms: 94
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 CAB C CAB R N N 0 3.211 -0.569 -1.456
2 CAC C CAC R N N 0 3.278 0.891 -1.811
3 CAD C CAD N N N 0 4.699 1.441 -1.633
4 CAE C CAE S N N 0 2.229 1.809 -1.29
5 CAF C CAF N N N 0 2.606 3.298 -1.505
6 CAG C CAG N N N 0 1.305 4.003 -1.092
7 CAH C CAH R N N 0 0.647 3.112 -0.036
8 CAI C CAI N N N 0 0.541 3.865 1.29
9 CAK C CAK N N N 0 -0.559 5.716 2.342
10 CAL C CAL N N N 0 1.632 1.945 0.064
11 CAM C CAM N N N 0 1.777 1.323 1.202
12 CAN C CAN R N N 0 2.787 0.267 1.53
13 CAO C CAO N N N 0 2.521 -0.122 3.006
14 CAP C CAP N N N 0 2.759 -1.633 2.911
15 CAQ C CAQ N N N 0 2.503 -2.013 1.478
16 CAR C CAR N N N 0 2.305 -3.433 1.021
17 CAS C CAS N N N 0 1.157 -4.067 1.809
18 CAT C CAT N N N 0 3.589 -4.23 1.26
19 CAU C CAU N N N 0 4.235 0.73 1.407
20 CAV C CAV N N N 0 2.405 -0.945 0.724
21 CAW C CAW R N N 0 1.955 -0.967 -0.717
22 CAY C CAY S N N 0 0.013 -0.652 -2.073
23 CBA C CBA R N N 0 -1.237 -2.029 -0.573
24 CBB C CBB N N N 0 -1.78 -3.449 -0.404
25 CBD C CBD N N N 0 -1.089 -5.728 -0.13
26 CBE C CBE R N N 0 -1.156 0.301 -2.303
27 CBF C CBF R N N 0 -2.075 0.343 -1.093
28 CBG C CBG S N N 0 -2.38 -1.069 -0.566
29 CBI C CBI S N N 0 -4.293 -0.274 -1.184
30 CBM C CBM S N N 0 -4.317 -0.329 0.375
31 CBN C CBN N N N 0 -5.466 -1.211 0.867
32 CBO C CBO S N N 0 -4.429 1.079 0.963
33 CBP C CBP N N N 0 -4.466 1.215 2.487
34 H1 H H1 N N N 0 -4.002 2.096 2.93
35 H10 H H10 N N N 0 -0.204 -6.36 -0.053
36 H11 H H11 N N N 0 -1.686 -5.826 0.776
37 H12 H H12 N N N 0 -1.681 -6.037 -0.991
38 H13 H H13 N N N 0 -5.267 -0.248 -1.671
39 H14 H H14 N N N 0 -1.664 0.973 -0.305
40 H15 H H15 N N N 0 -1.723 -0.034 -3.172
41 H16 H H16 N N N 0 -0.052 1.667 -3.312
42 H17 H H17 N N N 0 0.633 -0.689 -2.968
43 H18 H H18 N N N 0 1.693 -2.016 -1.006
44 H19 H H19 N N N 0 3.204 -1.137 -2.429
45 H2 H H2 N N N 0 -4.409 0.302 3.079
46 H20 H H20 N N N 0 4.447 -1.979 -0.684
47 H21 H H21 N N N 0 3.14 0.908 -2.942
48 H22 H H22 N N N 0 5.308 1.159 -2.492
49 H23 H H23 N N N 0 4.661 2.528 -1.557
50 H24 H H24 N N N 0 5.138 1.028 -0.725
51 H25 H H25 N N N 0 2.064 -3.442 -0.043
52 H26 H H26 N N N 0 3.829 -4.221 2.323
53 H27 H H27 N N N 0 3.445 -5.259 0.929
54 H28 H H28 N N N 0 4.407 -3.779 0.698
55 H29 H H29 N N N 0 1.397 -4.057 2.872
56 H3 H H3 N N N 0 -3.94 1.87 0.395
57 H30 H H30 N N N 0 0.242 -3.499 1.638
58 H31 H H31 N N N 0 1.013 -5.095 1.478
59 H32 H H32 N N N 0 2.061 -2.157 3.561
60 H33 H H33 N N N 0 3.784 -1.868 3.182
61 H34 H H34 N N N 0 1.497 0.103 3.275
62 H35 H H35 N N N 0 3.246 0.355 3.654
63 H36 H H36 N N N 0 4.887 -0.138 1.31
64 H37 H H37 N N N 0 4.34 1.364 0.526
65 H38 H H38 N N N 0 4.513 1.295 2.296
66 H39 H H39 N N N 0 1.056 1.557 2.007
67 H4 H H4 N N N 0 -6.416 -0.774 0.559
68 H40 H H40 N N N 0 1.346 1.677 -1.985
69 H41 H H41 N N N 0 3.409 3.589 -0.84
70 H42 H H42 N N N 0 2.829 3.482 -2.546
71 H43 H H43 N N N 0 1.531 4.979 -0.67
72 H44 H H44 N N N 0 0.651 4.102 -1.955
73 H45 H H45 N N N 0 -1.281 3.343 -0.601
74 H46 H H46 N N N 0 0.194 3.184 2.068
75 H47 H H47 N N N 0 1.52 4.26 1.563
76 H48 H H48 N N N 0 -0.929 5.074 3.142
77 H49 H H49 N N N 0 0.396 6.149 2.637
78 H5 H H5 N N N 0 -5.369 -2.208 0.438
79 H50 H H50 N N N 0 -1.278 6.514 2.156
80 H6 H H6 N N N 0 -5.433 -1.278 1.954
81 H7 H H7 N N N 0 -0.579 -1.801 0.266
82 H8 H H8 N N N 0 -2.391 -3.5 0.496
83 H9 H H9 N N N 0 -2.387 -3.711 -1.271
84 OAA O OAA N N N 0 4.395 -1.019 -0.789
85 OAJ O OAJ N N N 0 -0.386 4.944 1.153
86 OAX O OAX N N N 0 0.796 -0.187 -0.971
87 OAZ O OAZ N N N 0 -0.486 -1.96 -1.784
88 OBC O OBC N N N 0 -0.689 -4.366 -0.292
89 OBH O OBH N N N 0 -3.466 -1.459 -1.458
90 OBJ O OBJ N N N 0 -3.035 -0.921 0.709
91 OBK O OBK N N N 0 -0.648 1.613 -2.552
92 OBL O OBL N N N 0 -3.384 0.817 -1.508
93 OBQ O OBQ N N N 0 -5.624 1.411 1.673
94 OBR O OBR N N N 0 -0.628 2.642 -0.47



1F5 : Chemical Bonds

Total Number of Bonds: 100
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 OBR CAH O C sing 1.43 N N
2 CAP CAO C C sing 1.53 N N
3 CAP CAQ C C sing 1.5 N N
4 CAO CAN C C sing 1.55 N N
5 CAT CAR C C sing 1.53 N N
6 OAJ CAK O C sing 1.43 N N
7 OAJ CAI O C sing 1.43 N N
8 CAS CAR C C sing 1.53 N N
9 CAH CAI C C sing 1.53 N N
10 CAH CAL C C sing 1.53 N N
11 CAH CAG C C sing 1.53 N N
12 CAQ CAR C C sing 1.5 N N
13 CAQ CAV C C doub 1.31 N N
14 CAM CAL C C doub 1.3 E N
15 CAM CAN C C sing 1.5 N N
16 CAL CAE C C sing 1.49 N N
17 CAN CAV C C sing 1.5 N N
18 CAN CAU C C sing 1.53 N N
19 CAG CAF C C sing 1.54 N N
20 CAF CAE C C sing 1.55 N N
21 OBQ CBP O C sing 1.43 N N
22 OBQ CBO O C sing 1.43 N N
23 CAE CAC C C sing 1.49 N N
24 CAV CAW C C sing 1.51 N N
25 CBP CBO C C sing 1.53 N N
26 OBJ CBM O C sing 1.45 N N
27 OBJ CBG O C sing 1.44 N N
28 CBB CBA C C sing 1.53 N N
29 CBB OBC C O sing 1.43 N N
30 CBN CBM C C sing 1.53 N N
31 CBO CBM C C sing 1.53 N N
32 CBA CBG C C sing 1.49 N N
33 CBA OAZ C O sing 1.43 N N
34 CAW CAB C C sing 1.51 N N
35 CAW OAX C O sing 1.42 N N
36 CAC CAB C C sing 1.5 N N
37 CAC CAD C C sing 1.53 N N
38 CBM CBI C C sing 1.56 N N
39 CBD OBC C O sing 1.43 N N
40 CAB OAA C O sing 1.43 N N
41 CBG CBF C C sing 1.54 N N
42 CBG OBH C O sing 1.46 N N
43 OAX CAY O C sing 1.43 N N
44 OAZ CAY O C sing 1.43 N N
45 CBF OBL C O sing 1.45 N N
46 CBF CBE C C sing 1.52 N N
47 OBH CBI O C sing 1.47 N N
48 CBI OBL C O sing 1.46 N N
49 CAY CBE C C sing 1.53 N N
50 CBE OBK C O sing 1.43 N N
51 CBP H1 C H sing 1.09 N N
52 CBP H2 C H sing 1.09 N N
53 CBO H3 C H sing 1.09 N N
54 CBN H4 C H sing 1.09 N N
55 CBN H5 C H sing 1.09 N N
56 CBN H6 C H sing 1.09 N N
57 CBA H7 C H sing 1.09 N N
58 CBB H8 C H sing 1.09 N N
59 CBB H9 C H sing 1.09 N N
60 CBD H10 C H sing 1.09 N N
61 CBD H11 C H sing 1.09 N N
62 CBD H12 C H sing 1.09 N N
63 CBI H13 C H sing 1.09 N N
64 CBF H14 C H sing 1.09 N N
65 CBE H15 C H sing 1.09 N N
66 OBK H16 O H sing 0.97 N N
67 CAY H17 C H sing 1.09 N N
68 CAW H18 C H sing 1.12 N N
69 CAB H19 C H sing 1.13 N N
70 OAA H20 O H sing 0.97 N N
71 CAC H21 C H sing 1.14 N N
72 CAD H22 C H sing 1.09 N N
73 CAD H23 C H sing 1.09 N N
74 CAD H24 C H sing 1.09 N N
75 CAR H25 C H sing 1.09 N N
76 CAT H26 C H sing 1.09 N N
77 CAT H27 C H sing 1.09 N N
78 CAT H28 C H sing 1.09 N N
79 CAS H29 C H sing 1.09 N N
80 CAS H30 C H sing 1.09 N N
81 CAS H31 C H sing 1.09 N N
82 CAP H32 C H sing 1.09 N N
83 CAP H33 C H sing 1.09 N N
84 CAO H34 C H sing 1.08 N N
85 CAO H35 C H sing 1.08 N N
86 CAU H36 C H sing 1.09 N N
87 CAU H37 C H sing 1.09 N N
88 CAU H38 C H sing 1.09 N N
89 CAM H39 C H sing 1.11 N N
90 CAE H40 C H sing 1.13 N N
91 CAF H41 C H sing 1.08 N N
92 CAF H42 C H sing 1.08 N N
93 CAG H43 C H sing 1.09 N N
94 CAG H44 C H sing 1.09 N N
95 OBR H45 O H sing 0.97 N N
96 CAI H46 C H sing 1.09 N N
97 CAI H47 C H sing 1.09 N N
98 CAK H48 C H sing 1.09 N N
99 CAK H49 C H sing 1.09 N N
100 CAK H50 C H sing 1.09 N N



1F5 : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
1F5 4ihl Open in New Window Bound ligand 2 1